On my server (Emerald Dream) and I imagine most other servers since this shouldn't change much, I have specific cuts of each variety that sell best. For Stars of Elune, there's really only the solid star of elune cut that's worth having for profit, the others are just for personal or guild use.
For Noble Topaz, my best money making cut is Wicked Noble Topaz, followed closely by Potent Noble Topaz, Glinting sells well, but just not for as high a price.
For Living Rubies, Bright is the single best selling cut and for the highest price. A good alternate if you can't get bright living ruby is to get the Delicate Living Ruby cut, it's the agility cut and it sells just as fast as bright but for a slightly lower price (IE if bright goes for 75 like usualy, you can get 70 for delicate).
For Nightseyes there really hasn't been a best cut for me, I just cut whatever is going for the most that day. Balanced is a good cut to have just because not many people have it yet and you can control that market more easily. Glowing is always in demand but competition can drive the prices lower.
Dawnstones are the least expensive stones on my server, but smooth always sells for the most followed closely by Thick Dawnstones.
Lastly, Talasites vary for me. Usually I sell Jagged Talasites for the most, but sometimes Enduring will be a better choice, both sell well and usually won't expire unless a lot of people undercut me shortly after posting. Either of those cuts would be a good choice.
I think I've covered the whole range of rare stones but let me know if I missed one or if there are any questions. Oh yeah, and meta suck for profit purposes so I won't even bother listing them.
-Mont